The Psychology of The Wolverine
The film begins prior to the Weapon X experiment during World War II in a Japanese village. Wolverine saves a Japanese soldier from an honorable suicide and from an atomic bomb.

Then the scene switches to Logan waking up alone on a mountain. He lives alone from civilization, communes with bears, and occasionally walks into a tiny town for supplies. There he meets Yukio, a young woman who can tell the future. Yukio has searched for Logan, tasked with retrieving him for her employer Yashida. He is the soldier Logan saved during World War II, and now he is on his death bed. Reluctantly, Logan agrees to say goodbye to him in Japan.
Yashida passes away, and at the funeral, the mob attacks and kidnaps Mariko. Logan is hurt rescuing her and somehow does not heal. He suspects Yashida’s oncologist Dr. Green somehow stole his healing power.
In his will, Yashida left his enormous tech empire to his granddaughter Mariko, not his son. So not surprisingly Mariko is kidnapped again, and again Logan takes off to save her. He interrogates Noboru, Mariko’s finance, who confesses that he’s helping Shingen knock off Mariko so Shingen can have the inheritance.
While several parties play Markio hot potato, Logan attempts to regain his healing power by pulling a parasite out of his body himself. Then going to find Mariko, Logan fights Dr. Green and her adamantium samurai.
Guilt / Shame

The Wolverine takes place following X3: The Last Stand, in which Logan had to kill Jean Grey to stop her from basically destroying everything in sight. So throughout The Wolverine, Logan has visions of Jean in another place, wanting to be with her. The first time viewers see these visions, Logan tells Jean, “I’ll never hurt you, or anyone, ever again. I made a vow.” Despite hurting countless people for over a hundred years, having to kill someone he loved caused Logan enough trauma and guilt that he becomes a pacifist hermit. However, this vow doesn’t last very long.
Logan and Mariko at some point sleep together (What? They were into each other? Was I supposed to notice some sort of sexual tension? Ok.). Lying next to her, Logan still envisions Jean. Perhaps he feels guilt for sleeping with another woman, for romantically moving on, for being alive while Jean is dead.
He is so riddled with the multiple lifetimes of guilt that when shot with a poisoned arrow, Logan is bombarded with memories of Kayla, Mariko, and Jean all calling for help, all being hurt, mostly due to his involvement in some way.
Suicide
Yukio begins coaching Logan, preparing him for his meeting with Yashida that is, of course, not what it seems: “You are a solider, and you seek what all soldiers do. An honorable death. An end to your pain.” This honorable death in Japan is referred to as “seppuku,” once a suicidal ritual of samurais. When Logan first meets Yashida, he is considering seppuku like his other fellow soldiers rather than die by the atomic bomb, but Logan saves him.
Later Yashida offers Logan death—in essence, suicide—in exchange for his healing power. Although Logan refuses, he still has not necessarily suicidal ideations in the form of wanting to or imagining killing himself, but does have a desire for death. He dreams of Jean talking him into the exchange. At one point the vision of Jean tells him, “Just let it go. It’s not hard to die. Come to me."

The majority of the movie, viewers are led to believe that Yashida has died; however, Yashida has merely been relocated and now wears a life-sustaining adamantium samurai suit. Through the suit, Yashida—somehow—drains Logan’s healing power through his adamantium claws. As Logan ages, Yashida grows younger. To save Logan, Mariko kills Yashida, and once again Logan regains his healing power.
At this point, Logan passes out and envisions Jean one last time. He tells her that dying is not what he wants anymore, perhaps because he’s found a new reason to live. Talking to his vision, he works through his guilt over killing Jean. He tells her that he loves her, and she leaves, symbolizing that Logan has let go of his guilt and pain, and therefore has regained his desire to live.
If YOU are considering suicide, or know someone who may be, you can check out the Suicide Prevention Lifeline website or call 1-800-273-8255. Or if you just need a friend to talk to in a non-counseling capacity, you can chat me up.
Identity
Throughout the film, Logan rejects and takes on a variety of labels. At the beginning, a store clerk asks off-handedly, "You’re not a hunter, are you?” To which he cryptically replies, “Not anymore." As seen in other films, Logan has been a hunter, an assassin, a killer. But now he refuses that identity.
Yashida refers to Logan was Kuzuri, which means an animal with claws and sharp teeth, that fears nothing. While she was growing up, Mariko’s grandfather told her fairy tale type stories of Logan when she was little. Logan says he killed the Kuzuri at the same time that he killed Jean. But when Shingen attacks, he asks Logan, "What kind of monster are you?” Although not using the Japanese, Logan assumes his given identity and answers, “The Wolverine."
Despite statements that Logan wants to be alone and stay away from others, when Mariko tells him to leave her alone, he says he can’t because that means she’ll die. Logically Logan is not responsible for her life, the issue isn’t his problem, and she literally tells him to go away. Yet still, he protects her. Later, after fighting to protect Mariko, he envisions Jean again. The vision of Jean says, "That’s a lot of blood. I thought you were done trying to be a hero.” So previously Logan had rejected the identity of “hero” after killing Jean. Logan replies, “But those guys were trying to kill her.” Even in his pain, despite saying that he no longer wants to be a hero, Logan IS a hero and can’t help being anything but.

Instead of settling down and making a life with Mariko, Logan leaves Japan and Mariko, assumedly to return to the X-Men. At the beginning of the film, Yukio calls him a soldier. Now Logan says to Mariko, “I’m a soldier, and I’ve been hiding too long.”
While hiding in a village, Mariko tells Logan, “Everything in the world finds peace. Eventually. Man can recover from anything. Maybe you, too." I think Logan does eventually recover and finds peace, showing that if he can eventually let go of his guilt and pain and rediscover his sense of self, anyone can.